Hundreds of flights were delayed in cities across the country Tuesday because of a computer failure in the Federal Aviation Administration's system for processing flight plans.

A representative from the FAA said a software problem in the administration's central system for processing flight plans, based in an Atlanta office, caused the system to go down at about 1 p.m. EDT on Tuesday. That failure prompted a backup system in Salt Lake City to take over flight-plan processing, but a backlog in the handover caused flight delays instead, according to FAA officials.

"There were about 5,000 flight plans in the system, but a lot of them were airborne and unaffected," said Hank Krakowski, chief operating officer of the FAA's Air Traffic Organization. "The only flights that were affected were those that had already pushed off from the gates and couldn't get off the ground. It created a backlog."

The FAA said it expects the problem to be fixed by about 6:30 p.m. EDT.

The problem largely hit cities in the Midwest and on the East Coast, but the FAA was unable to be specific about how many airports or flights were affected. Those airports hit hardest by delays were in Boston, Atlanta, and the Washington, D.C. area. Washington National was still experiencing delays as of 6 p.m. EDT. Chicago O'Hare had experienced 60- to 80-minute delays throughout the afternoon. And Atlanta had as many as 40 aircraft backed up during the afternoon, according to FAA officials.

To put the software trouble in perspective, a bad day of thunderstorms might cause more flight delays than those experienced on Tuesday. But the FAA's computer issues likely had a larger geographical affect, officials said. Part of the work in diagnosing the computer failure will be in understanding why some airports were more affected than others, officials said.

"There were so many aircraft and flight plans...it overwhelmed the system. It rejected plans and increased delays, and added to the volume, so we're managing our way out of it," Krakowski said.

At the heart of the problem was the FAA's computer system known as NADIN, or National Data Interchange Network, which processes the flight plans that airlines file every day. The FAA always runs a parallel system in the event of a software glitch, but officials said that they had never encountered the challenge they had Tuesday.

"This was a failure mode we've not seen before.," Krakowski said, without describing the problem exactly. He added that the agency did not suspect any hacking or safety issues.

"It looks like an internal software processing error. We think we know what it is, but we have to do forensics on it to figure it out," he said.

By the end of this year, the FAA plans to upgrade the NADIN software. Representatives did not say how the software will improve on the current system, however.